R Notebook for BCB Assignment 2

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colnames(Fang_genotypes) <- Fang_genotypes[,1]

Error in `colnames<-`(`*tmp*`, value = c(441L, 446L, 447L, 443L, 444L,  : 
  'names' attribute [2783] must be the same length as the vector [986]

First set of instructions: Describe file structures and their dimensions (file size, number of columns, number of lines, ect…). You don’t have to limit yourselves to the functions we learned in class.

As a reminder, the files are: • fang_et_al_genotypes.txt: a published SNP data set including maize, teosinte (i.e., wild maize), and Tripsacum (a close outgroup to the genus Zea) individuals • snp_position.txt: an additional data file that includes the SNP id (first column), chromosome location (third column), nucleotide location (fourth column) and other information for the SNPs genotyped in the fang_et_al_genotypes.txt file

Fang_genotypes

View(Fang_genotypes)

Add in name to all columns in fang et all genotypes

names(Fang_Genotypes)[1]<-paste("SNP_ID")
names(Fang_genotypes)[2]<-paste("Gene")
names(Fang_genotypes)[3]<-paste("Group")

snp_names <- data.frame(Fang_genotypes[,1])

extract maize genes for ZMMIL, ZMMLR, and ZMMMR and teos genes for ZMPBAL, ZMPIL, ZMPJA

dim(maize_genes)

[1] 1546  986

Now we will manipulate the two files to join (these data sets so that we have both genotypes and positions formatted such that the first column is “SNP_ID”, the second column is “Chromosome”, the third column is “Position”, and subsequent columns are genotype data from either maize or teosinte individuals.

Extract out the genes from the joined file that we want for maize

Maize_genes_to_extract1 <- c('ZMMIL','ZMMLR', 'ZMMMR')

extract teosinte genes for ZMPBA, ZMPIL , ZMPJA

head(joined_genos)
Teos_genes_to_extract2 <- c('ZMPBA','ZMPIL','ZMPJA')  
teo_genes <- 

Genotype_subset_teos <- subset(Transposed_Genotypes, grep(Teos_genes_to_extract2))

Error in grep(Teos_genes_to_extract2) : 
  argument "x" is missing, with no default